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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtttagtacctcaagcagttcagaccattaattttcaagctgttatccatcatttctgaccatgttcttgttcatgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTTGAGCAGATGATAAGGGAGGCGGATACCGATGGCGACGGGCAGGTGAACT

Basic information

species Oryza sativa
transcript LOC_Os03g53200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G149923_T01 (Zea mays), 3'ss of exon 3
---gtggtttagtacctcaagcagttcagaccattaattttcaagctgttatccatcatttctgac--catgttcttg--ttcatgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTTGAGCAGATGATAAGGGAGGCGGATACCGATGGCGACGGGCAGGTGAACT
   ||   || || ||||    |  || ||||||    |  | |||||||  |  ||||   ||    | ||||  ||  ||  |||||| |||||||||| |||||||||| ||| |||||||||||||| |||||||||||||| |||||||| ||||| || || ||||| || ||||| ||||||||||
gtagtctctttgtgcctcggcaacctcggaccat--gctagctagctgtttccattcatccttgctttcgtgttggtgacttggtgtgtgaagCTGAGGACGGTGATGACCAGTCTCGGGGAGAAGATGACCGACGAGGAGGTTGAACAGATGATCAGGGAAGCAGACACCGACGGTGACGGTCAGGTGAACT

upper sequence: LOC_Os03g53200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ14591 (Selaginella moellendorffii), 3'ss of exon 3
gtggtttagtacctcaagcagttcagaccattaattttcaagctgttatccatcatttctgaccatgttcttgttcatgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTTGAGCAGATGATAAGGGAGGCGGATACCGATGGCGACGGGCAGGTGAACT
        || |    ||       ||   ||  | ||     |  | ||| |  |  |||||     | |  | |       ||| |||||   ||||||| |||||| || |||||| |||| ||||||||||| ||| |||||||  | ||||| || |  || |||||||| || || ||||
--------gt-ctgtgagagacatggattcttggtcttgtttttcgtttcctttttgactgactggaatttcttcc-------cagTTGAGGGACGTGATGATCAATCTGGGCGAGAAGCTGACCGACGAGGAGGTAGAGGAGATGATCCGCGAGGCTGACATGGACGGCGACGGTCACGTTAACT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86839294|gb|CI331547.1|CI331547
EST:     TTCGAGGTCCTAGAC-AGGATCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
genomic: TTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
EST: gi|38472151|gb|CF956282.1|CF956282
EST:     CTTTTGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
genomic: CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
EST: gi|29667976|gb|CB664251.1|CB664251
EST:     CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
genomic: CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
EST: gi|88329564|gb|CI650016.1|CI650016
EST:     CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACG
genomic: CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACG
EST: gi|88299406|gb|CI572358.1|CI572358
EST:     CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGA
genomic: CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGA
EST: gi|86833039|gb|CI333638.1|CI333638
EST:     TCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACACTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
genomic: TCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
EST: gi|88486058|gb|CI423329.1|CI423329
EST:     ATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
genomic: ATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
EST: gi|88404677|gb|CI581113.1|CI581113
EST:     TTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACCTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGAT
genomic: TTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAAC-TGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGAT
EST: gi|88407027|gb|CI581114.1|CI581114
EST:     CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGAACAATCTTGGGGAGAAGATG
genomic: CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATG
EST: gi|58589123|gb|CF987431.1|CF987431
EST:     CTTTTGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
genomic: CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
EST: gi|88471830|gb|CI409101.1|CI409101
EST:     CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
genomic: CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
EST: gi|86833041|gb|CI333640.1|CI333640
EST:     AATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
genomic: AATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
EST: gi|88404667|gb|CI581103.1|CI581103
EST:     CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG                         CTGAGGACCGTGATGACCAATCTTGGGGAGAAGATGACA
genomic: CTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACA
EST: gi|88432096|gb|CI562927.1|CI562927
EST:     ATGGTTTTATCTCCCCAACTGAG                         CTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT
genomic: ATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 75 (downstream exon)
Score: 26

GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAGgtggtttagt ... atgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTTGAGCAGATGATAAGGGAGGCGGATACCGATGGCGACGGGCAGGTGAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttcaagctgttatccatcatttctgaccatgttcttgttcatgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTTGAGCAGATGATAAGGGAGGCGGATACCGATGGCGACGGGCAGGTGAACT
                         ttctgac  putative branch site (score: 26)
                    atcattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtttagtacctcaagcagttcagaccattaattttcaagctgttatccatcatttctgaccatgttcttgttcatgtgtgcagCTGAGGACAGTGATGACCAATCTTGGGGAGAAGATGACAGACGAGGAGGTTGAGCAGATGATAAGGGAGGCGGATACCGATGGCGACGGGCAGGTGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG